Genetic factors contribute substantially to nicotine dependence; and recent meta-analyses of genome-wide association studies (GWAS) have identified polymorphisms that alter risk for nicotine dependence and have provided significant insights into the molecular basis of this dependency (Berrettini et al., 2008; Liu et al., 2010; Thorgeirsson et al., 2008; Thorgeirsson et al., 2010; Tobacco and Genetics Consortium, 2010). However, the variants found to date explain only a modest fraction of the genetic component of nicotine dependence. The goal of this proposal is to comprehensively catalogue genetic variation in the nicotinic receptors and nicotine metabolizing genes and to identify variants in these targeted regions that influence the development of nicotine dependence. To accomplish the goals of this proposal, we request custom targeted sequencing to catalogue variation in the nicotinic receptors and nicotine metabolizing genes (CYP2a6) in nicotine dependent and non-nicotine dependent subjects. The sample is racially diverse and includes 1,500 subjects of European descent and 1,500 subjects of African descent, all of whom have undergone a comprehensive phenotypic assessment. Using methods from comparative and functional genomics, we will apply state-of-the-art bioinformatics tools to classify all variants (coding and non-coding) for putative biologic function. Potential functional variants will be prioritized in our subsequent analyses. We will test common, moderate, and rare variants for association with nicotine dependence status using state of the art analytic approaches. Common variants will be analyzed by standard methods and less common variants (<5%) will be analyzed by collapsing methods. Variants will be prioritized based on putative biological function. By capitalizing on well-characterized case and control samples of phenotypic extremes of nicotine dependence and placing the deep sequencing program within our existing research program, this study will take an important next step along the cutting edge of genomic science and move the field to the next level of understanding the genetics of nicotine dependence.